I think the PW/PL crossover actually takes place in before the "present-day" Layton timeline (Curious Village, Diabolical Box, Unwound Future). At least, the design for Luke is the young design found in the prequel trilogy.
Last Specter, Eternal Diva (Movie 1), Mask of Miracle, Unnamed Movie 2, Advanced Civilization (announced today), Professor Layton vs. Phoenix Wright, Curious Village, Diabolical Box, Unwound Future.
I'm pretty sure that's how it goes chronologically. I'm taking a guess about the crossover, but that guess is based on what I've seen of Luke's design in that game. It's the same one from Last Specter through Mask of Miracle.
But yeah, I wish they'd do a chronological sequel to Unwound Future to finish the series. Then again, that game's plot was so unbelievably engaging, it'd be hard to top it. But the series deserves some sort of grandiose closure plot-wise.